medical/radiobiology/README.md

0001 \page Exampleradiobiology Example radiobiology
0002
0003 \author L Pandola, D Chiappara, GAP Cirrone, G Petringa, A Sciuto, S Fattori; - INFN LNS (Italy) \n
0004
0005 Radiobiology is an application realized for dosimetric and radiobiological applications of proton and ion beams.
0006 Specific tools were built to evaluate primaries and secondary energy spectra and a set of classes, dedicated to
0007 the computation of biological, as LET (Linear Energy Transfer), RBE (Relative Biological Effectiveness), Survival
0008 Fraction, and physical (as dose and fluence) quantities were implemented.
0009
0010 ## 1- GEOMETRY DEFINITION
0011
0012 The physical and dosimetric quantities are calculated in the water tank by scoring every quantity in each of the
0013 slices, representing a customizable (in terms of dimensions and materials) volume that can be voxelized depending
0014 on the user's needs.
0015
0016 In the proposed example, the “default” water tank represents a phantom typically used in the clinical hadrontherapy
0017 practice, to reconstruct the dose profile distributions in water.
0018 The phantom has a standard dimension of 4 x 4 x 4 cm and was sectioned into 0.2 x 40 x 40 mm slices (See Figure 1).
0019 The voxel dimensions can be user defined and can vary from 1um to 1 mm
0020 The source is positioned on one of the faces of the box
0021
0022 The default macro uses the default geometry configuration mentioned above with a simple run of 100k protons with a
0023 Gaussian energy distribution with a mean of 62 MeV and a standard deviation of 0.65 MeV
0024 The visualize.mac just creates a teest geometry and opens visualization
0025
0026 ## 2- PHYSICS LIST
0027
0028 In Radiobiology it is possible to activate three physics lists that are those already recommended for medical physics
0029 applications and that cover all the physics processes needed for a correct simulation in this field.
0030
0031 The electromagnetic interactions are modeled using the G4EmStandardPhysics_option4 constructor, which uses a
0032 condensed history algorithm based on the Beth-Bloch energy loss formula. This physics constructor was created for
0033 applications requiring high accuracy in electron, hadron, and ion tracking. It contains the most accurate standard
0034 and low-energy models and is recommended for simulations focused on medical physics applications.
0035 The hadronic interactions are simulated using models implemented in the QGSP BIC and QGSP BIC HP constructors,
0036 which employ Geant4 native preequilibrium and de-excitation models as low energy stages of the Binary Cascade model
0037 for protons, neutrons, and ions. The QGSP BIC HP constructor uses, in addition, the high precision neutron package
0038 (ParticleHP) to transport neutrons and light-charged particles with energies from 20 MeV down to thermal energy.
0039
0040 Production cuts for secondary generation are an important element in any MC simulation. It has a significant impact
0041 on energy deposition, particularly when small quantities are examined. The production cut in Geant4 is a distance
0042 (given in units of length), and secondary particles (electrons, positrons, gammas, and secondary protons) are only
0043 monitored if their expected range in that medium is greater than the imposed cut. Otherwise, secondary energy is
0044 not tracked and is deposited in the secondary production position. The cut for this example is achieved through
0045 the standard Geant4 implementation.
0046 ```
0047  /run/setCutForAGivenParticle e- 0.1 mm
0048  /run/setCutForAGivenParticle e+ 0.1 mm
0049  /run/setCutForAGivenParticle proton 0.1 mm
0050 ```
0051
0052 ## 3- LET CALCULATION
0053
0054 Radiobiology simulates and calculates the averaged LET-dose and LET-track fully accounting for the contribution of
0055 secondary particles generated in the target fragmentation
0056 Dependencies as respect to the transport parameters adopted during the Monte Carlo simulations as the production cut
0057 of secondaries particles, voxel size and the maximum steps length are minimized in the LET calculation.
0058 At run time, data needed to calculate LET are collected. At the end of simulation, LET mean values are calculated
0059 and stored into a file.
0060
0061 The Let.out file will be produced at the end of a run, where you can
0062 find the dose and track average LET for each tracked particles (both primary and
0063 secondary ones) and the total mean LET.
0064
0065 The file is structured as follows:
0066      - The first three columns contain the voxel indexes (first index "i" refers to the beam direction);
0067      - The fourth and fifth columns contain respectively total mean dose LET (LDT) and total mean track LET (LTT)
0068      - The rest of columns contain LET Dose and Track for each single ion (whose name is in the top row of the file).
0069
0070 ## 4- RBE and Survival calculation
0071
0072 A method was developed to assess the biological damages produced by proton and ion beams in terms of survival
0073 fraction curves, i.e of the number of cells able to survive after the irradiation at different dose. The approach
0074 is based on the combined use of Monte Carlo Geant4 simulations (to calculate the doses deposited and the energy
0075 spectra of particles interacting with cells) and of the Survival analytical code (Manganaro L, Russo G, et al.
0076 Survival: a simulation toolkit introducing a modular approach for radiobiological evaluations in ion beam therapy.
0077 Phys. Med. Biol. 2018;63(8). 08–01).
0078 The Monte Carlo simulations permit the calculation of the Edep and Ekin distributions that, coupled with the
0079 radiobiological response model, allow the final and calculation of a survival curve.
0080 The kinetic energy and the LET value of any primary ion and of the secondaries generated in each slice of the
0081 simulated water phantom are retrieved at each simulation step. The corresponding values of αi and βi, for each
0082 specific ion i with a kinetic energy Ei and a released dose Di, are then calculated by direct linear interpolation
0083 of the Look-up-tables provided by the Survival analytical code.
0084 (G.Petringa et al., Physica Medica 58 (2019) 72–80)
0085
0086 The AlphaAndBeta.out and RBE.out files are produced at the end of the run.
0087 AlphaAndBeta.out contains the average alpha (first column) and beta (second column) parameters calculated for each
0088 slice (third column).
0089
0090 RBE.out contains the following quantities:
0091     - Dose (Gy): the physical dose;
0092     - ln(S): the natural log of the Survival Fraction;
0093     - Survival Fraction;
0094     - DoseB (Gy): the biological dose;
0095     - RBE: relative biological effectiveness;
0096     - depth (slice): n. of the slice;